Mass spectrometry has evolved into an important analysis technique for biologically important species. The development of soft ionization methods has permitted mass analysis for large molecules and tandem mass spectrometry has been employed to obtain structural information for these molecules. Unfortunately, mass spectrometry alone cannot provide unequivocal structure elucidation. However, infrared spectroscopy provides complementary information which could be correlated with mass spectrometry measurements to permit unequivocal structure determination. The goal of this proposal is to develop instrumentation and methodologies for obtaining infrared spectra for mass selected ions formed by a mass spectrometer ion source. The proposed apparatus combines the advantages of mass selection using a quadrupole mass filter with the analyte concentrating feature of matrix isolation. Ions to be studied will be selected using a quadrupole mass filter and then deposited into an argon matrix at cryogenic temperatures. Infrared analysis will be performed by Fourier transform infrared spectroscopy. The apparatus will be tested using well-behaved systems and then applied to structure elucidation for various biologically important parent and daughter ions. Infrared spectral information will be correlated with mass spectrometric measurements in order to facilitate unequivocal structure elucidation.